The main character, Kira, who has a deformed leg, is recently orphaned since her mother abruptly died from unknown sickness, and her father died years ago on a hunt with the Hunters by being killed by The Beasts. Kira must learn to survive in a society that normally leaves the weak or disabled exposed to die in the fields.
Kira needs a reason for the council to keep her in the village and not to take her to the Field, which is certain death at the hands of The Beasts. A member of the council, Jamison, defends Kira during the trial, much to Kira's surprise, and convinces the Council that Kira has a gift for embroidery. She is found worthy of life in society at the trial and is given the task of repairing the Singer's robe.
She is taught how to further solidify her talent from a much older woman, Annabella, who continues to teach Kira how to create dyes for different shades and hues for her thread work. To Kira's dismay, she learns that there is no ability to create the color blue for the threads that she will be using. Eventually, to Kira's surprise, Annabella tells her that with her own years and knowledge, she knows much of the society's history and even goes so far as to say that there really are no Beasts, contrary to the society's beliefs. Kira is unsure what to think of that revelation or what Annabella really means by it.
Along the way, she becomes closer friends with a younger boy, Matt, and makes a new friend in her neighborhood at her new home, Thomas, who is a boy around Kira's age. Thomas is also an orphan and has lived there since he was very young because of his abilities. Kira learns that he is the woodworker who maintains and improves the Singer's staff, which, in turn, helps the Singer remember the history of the society as he sings the lengthy song. Together, they help each other bring out the best in their talents to prepare for The Gathering. Jamison, the Guardian who fought for her life in the trial, becomes somewhat of a mentor in her new home. He is kind and instructive but also very stern.
Kira slowly learns that her life is less than idyllic. Thomas hears crying in her building, and they discover another orphan, a very young girl, Jo, whose ability to sing is magnificent. She is kept with the intent of eventually replacing the current Singer. Jo is scolded and punished if she does not sing. Kira secretly befriends her and sneaks into Jo's locked room at night to comfort her. Kira realizes that the three do not have as much freedom as they had previously thought. Annabella abruptly dies, and Matt tells Kira that the old dyer had died and been dragged to the Field by Jamison and his men. Kira is later told by Jamison that Annabella had died of old age in her sleep. Kira is left to continue her work. That, and the secluded life that a very young Jo must live, help Kira decide to find out the truth about her society.
On the day that the Singer sings the Song at the Gathering, Matt is nowhere to be found. At the Ceremony of the Gathering, she notices that the current Singer both uses the staff that Thomas has worked so hard on and wears the robe that she repaired and enhanced. She realizes that his feet are chained, scarred, and bleeding. This implies that he is essentially a prisoner kept for the Ceremony because of his talent. This implies that Kira and the others with Gifts, which the council has saved for their jobs, are also prisoners. Their gifts are in control of the council by tenants who, without any creativity of their own, seek to control the three to provide a future that they envision.
After a long absence, Matt returns with a blind man from the distant Village of Healing. The man wears a blue shirt, which Kira's people are unable to make. The man is Kira's father, Christopher, who Kira long thought dead. Christopher reveals that he had been attacked years earlier by another hunter, who was jealous of his immediate potential of being a member on the Council of the Guardians. He was beaten and stabbed, blinding him. After being taken to the fields to die with the other rejected, injured, and dying citizens of their society, he was rescued by some people he could not see. They took him to the Village that he now lives in. This village is full of kind and helpful people, as opposed to the selfish residents of Kira's village. Matt excitedly explains that they know the way to make blue threads, and he brings plants that will allow Kira to do the same.
After a long heartfelt reunion with his daughter, Christopher reveals that he has enemies on the council. The one who maimed him years before was none other than Jamison. He tearfully apologizes for taking so long to return to get her. Because of his memory loss caused by the beating and his loss of sight, he had no way of finding her. Matt had gone looking for a way to make blue for Kira and stumbled upon Christopher's village, leading to this eventual reunion.
Kira begins to wonder if her mother's sudden death and the deaths of the two other orphans' parents were actually by the council's hand to acquire the young gifted children so that it could mould them into creating the future that it wants.
Christopher cannot stay and is forced to return to his village. Kira, however, decides to stay in her own community to continue to embroider the Singer's robe and help improve her society. Matt is designated as the "eyes" that will help Christopher find his way back. It is implied that Thomas, Kira, and Jo, who are the new holders of the Gifts, have the opportunity to change the cycle of their society and to improve the conditions in which they live by using their gifts to influence the actions of their people vastly.
At the end of the book, Matt tells Kira that in the Village, all are important and married, which she would have to do without in her society in which the injured and the impaired are seen as worthless wastes of space. He continues to tell her about a boy from the Village who has blue eyes, is around her age, and is not injured in any way (alluding to Jonas from The Giver) in the hope that will entice her to come with them. Kira declines to go with them to the Village, but it is decided that she will follow once her work in her current task is eventually finished. In the meantime, Matt will travel back and forth between Kira and her father Christopher, being called their Messenger, relaying their messages.
